Interpretive Summary: The Southern root-knot nematode (RKN) is a major pest of cotton in the United States. Moderately resistant varieties are available, but no highly resistant varieties are available to growers. Germplasm with a high level of resistance has been available to companies producing varieties, but conventional breeding for resistance involves many tests in greenhouses or fields where plants are infected with nematodes and scored for level of resistance. This is very time consuming and expensive. Recently, molecular markers on chromosomes 11 and 14 have been associated with RKN resistance, thus opening the way for marker assisted selection (MAS) in applied breeding. Our study aimed to determine the utility of these markers for MAS. Cross one was RKN resistant germplasm M240 RNR × the susceptible cultivar FM966 and is representative of the initial cross a breeder would make to develop a RKN resistant cultivar. Cross two consists of Clevewilt 6 × Wild Mexico (PI563649), which are the two lines originally used to develop the first highly RKN resistant germplasm. We phenotyped the F2 of cross one for gall index and number of RKN eggs per plant and genotyped each plant for markers CIR 316 (chromosome 11) and BNL 3661(chromosome 14). From this, we verified that MAS was effective, and the QTL on chromosome 14 was primarily associated with a dominant RKN resistance gene affecting reproduction. In the first F2 population of cross two, we used MAS to identify 11 plants homozygous for the markers on chromosomes 11 and 14, and which also flowered in long days. Progeny of these 11 plants were phenotyped for RKN gall index and egg number and confirmed as RKN highly resistant plants. Generally about 7-10 generations of RKN phenotyping and progeny testing were required in the 1960’s to develop the original RKN highly resistant population. Commercial breeders should be able to use the markers in MAS to rapidly develop RKN resistant cultivars.

Technical Abstract:
Cotton (Gossypium hirsutum L) cultivars highly resistant to the southern root-knot nematode (RKN) [Meloidogyne incognita (Kofoid & White) Chitwood] are not available. Recently, molecular markers on chromosomes 11 and 14 have been associated with RKN resistance, thus opening the way for marker assisted selection (MAS) in applied breeding. Our study aimed to determine the utility of these markers for MAS. Cross one was RKN resistant germplasm M240 RNR × the susceptible cultivar, FM966 and is representative of the initial cross a breeder would make to develop a RKN resistant cultivar. Cross two consists of Clevewilt 6 × Wild Mexico (PI563649), which are the two lines originally used to develop the first highly RKN resistant germplasm. We phenotyped the F2 of cross one for gall index and number of RKN eggs per plant and genotyped each plant for CIR 316 (chromosome 11) and BNL 3661(chromosome 14). From this, we verified that MAS was effective, and the QTL on chromosome 14 was primarily associated with a dominant RKN resistance gene affecting reproduction. In the first F2 population of cross two, we used MAS to identify 11 plants homozygous for the markers on chromosomes 11 and 14, and which also flowered in long days. Progeny of these 11 plants were phenotyped for RKN gall index and egg number and confirmed as RKN highly resistant plants. Generally about 7-10 generations of RKN phenotyping and progeny testing were required in the 1960’s to develop the original RKN highly resistant population. Commercial breeders should be able to use the markers in MAS to rapidly develop RKN resistant cultivars.